SMaSH: a benchmarking toolkit for human genome variant calling

MOTIVATION Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. RESULTS We propose SMaSH, a benchmarking methodology for evaluating germline variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on these benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single-nucleotide polymorphism, indel and structural variant calling algorithms. AVAILABILITY AND IMPLEMENTATION We provide free and open access online to the SMaSH tool kit, along with detailed documentation, at smash.cs.berkeley.edu